Bariatric Run Notebook

An analysis of the MBSA-QIP Dataset

Author

Affiliations

Pranav Kumar Mishra

Dept of Surgery, Rush University

Dept of Orthopedic Surgery, Rush University

An Exception was encountered at ‘In [19]’.

The computer’s name is pminformatics.rush.edu The current directory has been set to /home/pranav/work/pranavmishra90/courses/by-mishra/research-data-management

Caution: The run directory already exists for Run # 001 A figures directory is already present: /home/pranav/work/pranavmishra90/courses/by-mishra/research-data-management/data/analysis/bariatric/runs/run_001/figures/ A tables directory is already present: /home/pranav/work/pranavmishra90/courses/by-mishra/research-data-management/data/analysis/bariatric/runs/run_001/tables/ A notebook directory is already present: /home/pranav/work/pranavmishra90/courses/by-mishra/research-data-management/data/analysis/bariatric/runs/run_001/notebooks/ A text directory is already present: /home/pranav/work/pranavmishra90/courses/by-mishra/research-data-management/data/analysis/bariatric/runs/run_001/text/

Import Data

Statistics for Main dataframe

There are 1,021,936 cases with 245 variables (columns).

Data Processing

Subset the data

Filtering for CPT: ['43644']

The total MBSA-QIP dataset mbsa_main_df has 1,021,936 cases.

After filtering, 269,926 cases remain in the dataset mbsa_df

Generate Figures and Tables

Age

'Figure saved to /home/pranav/work/pranavmishra90/courses/by-mishra/research-data-management/data/analysis/bariatric/runs/run_001/figures//demographics/Run001_Demographics-Donor_Sex.jpg'

'Figure saved to /home/pranav/work/pranavmishra90/courses/by-mishra/research-data-management/data/analysis/bariatric/runs/run_001/figures//demographics/Run001_Demographics-Race.jpg'

'Figure saved to /home/pranav/work/pranavmishra90/courses/by-mishra/research-data-management/data/analysis/bariatric/runs/run_001/figures//demographics/Run001_Demographics-Ethnicity.jpg'

'Figure saved to /home/pranav/work/pranavmishra90/courses/by-mishra/research-data-management/data/analysis/bariatric/runs/run_001/figures//surgery/Run001_Sx-OPLENGTH_PREVSURG.jpg'

Save the run dataset

Execution using papermill encountered an exception here and stopped:

PermissionError: [Errno 13] Permission denied: '/home/pranav/work/pranavmishra90/courses/by-mishra/research-data-management/data/analysis/bariatric/runs/run_001/tables///Run001_main_dataset.parquet'